AMBER Archive (2009)

Subject: Re: [AMBER] xleap-does not work

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Sat Oct 10 2009 - 08:35:53 CDT

Dear Prof. Case,

Thanks for your remind, it seems that I have been obsolete, I always thought there should be not change in amber10 and amber9 in such basic operation. Before, when I used amber9, these force parameters were loaded automatically. After I load the force field one by one using source, the protein can be load without complain. But another problem is still cannot be solved:
I open a window, using "edit a"
then I chose several atoms and want to edit them in the window. However, when I chose "edit" on the top of the window, and click "edit selected atoms", there was no response. I remembered when I used amber9, I ever came across this problem. after I restart my computer this problem could be solved. But this time it did not work.

Can you give me some help again?

Thanks for your help again!

Rilei Yu

--- 09年10月10日，周六, case <case_at_biomaps.rutgers.edu> 写道：

发件人: case <case_at_biomaps.rutgers.edu>
主题: Re: [AMBER] xleap-does not work
收件人: "AMBER Mailing List" <amber_at_ambermd.org>
日期: 2009年10月10日,周六,下午8:27

On Sat, Oct 10, 2009, Rilei Yu wrote:
>
> After failing many times to install the amber10 in the ubuntu, I decided
> to install it again, this afternoon. Today, I installed it step by step
> based on the tutorial on our forum. After finished the whole process,
> I found the xleap still did not work. When I load the pdb (completely
> normal residues) from database, I found all the atom were not recognized
> by amber!

We need more information: you need to say exactly what commands you typed
to "load the pdb".  Also, have you run the tutorials?  My (wild?) guess is
that you did not properly load a force field, and the tutorials (esp. tutorial
B1) illustrate how to do that.

...dac

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